Merge pull request #57 from moshi4/develop

Bump to v1.3.0

.github/workflows/ci.yml

@@ -19,17 +19,12 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      # - name: Setup Python ${{ matrix.python-version}}
-      #   uses: actions/setup-python@v5
-      #   with:
-      #     python-version: ${{ matrix.python-version }}
-
       - name: Install Rye
         run: |
           curl -sSf https://rye.astral.sh/get | RYE_INSTALL_OPTION="--yes" bash
           echo "$HOME/.rye/shims" >> $GITHUB_PATH
 
-      - name: Install python dependencies
+      - name: Setup Python ${{matrix.python-version}} & Dependencies
         run: |
           rye pin ${{ matrix.python-version }}
           rye sync --update-all --all-features

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.1
+    rev: v0.5.6
     hooks:
       - id: ruff
         name: ruff lint check

requirements-dev.lock

@@ -7,6 +7,7 @@
 #   all-features: true
 #   with-sources: false
 #   generate-hashes: false
+#   universal: false
 
 -e file:.
 altair==5.3.0
@@ -15,23 +16,25 @@ asttokens==2.4.1
     # via stack-data
 astunparse==1.6.3
     # via griffe
-attrs==23.2.0
+attrs==24.1.0
     # via jsonschema
     # via referencing
 babel==2.15.0
     # via mkdocs-material
 backcall==0.2.0
     # via ipython
+backports-strenum==1.3.1
+    # via griffe
 beautifulsoup4==4.12.3
     # via nbconvert
 biopython==1.83
     # via pygenomeviz
-black==24.4.2
+black==24.8.0
 bleach==6.1.0
     # via nbconvert
 blinker==1.8.2
     # via streamlit
-cachetools==5.3.3
+cachetools==5.4.0
     # via streamlit
 certifi==2024.7.4
     # via requests
@@ -55,7 +58,7 @@ coverage==7.6.0
     # via pytest-cov
 cycler==0.12.1
     # via matplotlib
-debugpy==1.8.2
+debugpy==1.8.3
     # via ipykernel
 decorator==5.1.1
     # via ipython
@@ -79,13 +82,13 @@ gitdb==4.0.11
     # via gitpython
 gitpython==3.1.43
     # via streamlit
-griffe==0.47.0
+griffe==0.48.0
     # via mkdocstrings-python
 identify==2.6.0
     # via pre-commit
 idna==3.7
     # via requests
-importlib-metadata==8.0.0
+importlib-metadata==8.2.0
     # via jupyter-client
     # via markdown
     # via mkdocs
@@ -127,7 +130,7 @@ jupyter-core==5.7.2
     # via nbformat
 jupyterlab-pygments==0.3.0
     # via nbconvert
-jupytext==1.16.3
+jupytext==1.16.4
     # via mkdocs-jupyter
 kiwisolver==1.4.5
     # via matplotlib
@@ -171,13 +174,13 @@ mkdocs-autorefs==1.0.1
 mkdocs-get-deps==0.2.0
     # via mkdocs
 mkdocs-jupyter==0.24.8
-mkdocs-material==9.5.28
+mkdocs-material==9.5.31
     # via mkdocs-jupyter
 mkdocs-material-extensions==1.3.1
     # via mkdocs-material
-mkdocstrings==0.25.1
+mkdocstrings==0.25.2
     # via mkdocstrings-python
-mkdocstrings-python==1.10.5
+mkdocstrings-python==1.10.7
     # via mkdocstrings
 mypy-extensions==1.0.0
     # via black
@@ -245,15 +248,15 @@ pluggy==1.5.0
 pre-commit==3.5.0
 prompt-toolkit==3.0.47
     # via ipython
-protobuf==5.27.2
+protobuf==5.27.3
     # via streamlit
 psutil==6.0.0
     # via ipykernel
 ptyprocess==0.7.0
     # via pexpect
-pure-eval==0.2.2
+pure-eval==0.2.3
     # via stack-data
-pyarrow==16.1.0
+pyarrow==17.0.0
     # via streamlit
 pydeck==0.9.1
     # via streamlit
@@ -263,12 +266,12 @@ pygments==2.18.0
     # via mkdocs-material
     # via nbconvert
     # via rich
-pymdown-extensions==10.8.1
+pymdown-extensions==10.9
     # via mkdocs-material
     # via mkdocstrings
 pyparsing==3.1.2
     # via matplotlib
-pytest==8.2.2
+pytest==8.3.2
     # via pytest-cov
 pytest-cov==5.0.0
 python-dateutil==2.9.0.post0
@@ -288,23 +291,23 @@ pyyaml==6.0.1
     # via pyyaml-env-tag
 pyyaml-env-tag==0.1
     # via mkdocs
-pyzmq==26.0.3
+pyzmq==26.1.0
     # via ipykernel
     # via jupyter-client
 referencing==0.35.1
     # via jsonschema
     # via jsonschema-specifications
-regex==2024.5.15
+regex==2024.7.24
     # via mkdocs-material
 requests==2.32.3
     # via mkdocs-material
     # via streamlit
 rich==13.7.1
     # via streamlit
-rpds-py==0.19.0
+rpds-py==0.19.1
     # via jsonschema
     # via referencing
-ruff==0.5.1
+ruff==0.5.6
 six==1.16.0
     # via asttokens
     # via astunparse
@@ -316,7 +319,7 @@ soupsieve==2.5
     # via beautifulsoup4
 stack-data==0.6.3
     # via ipython
-streamlit==1.36.0
+streamlit==1.37.0
     # via pygenomeviz
 tenacity==8.5.0
     # via streamlit

requirements.lock

@@ -7,18 +7,19 @@
 #   all-features: true
 #   with-sources: false
 #   generate-hashes: false
+#   universal: false
 
 -e file:.
 altair==5.3.0
     # via streamlit
-attrs==23.2.0
+attrs==24.1.0
     # via jsonschema
     # via referencing
 biopython==1.83
     # via pygenomeviz
 blinker==1.8.2
     # via streamlit
-cachetools==5.3.3
+cachetools==5.4.0
     # via streamlit
 certifi==2024.7.4
     # via requests
@@ -81,9 +82,9 @@ pillow==10.4.0
     # via streamlit
 pkgutil-resolve-name==1.3.10
     # via jsonschema
-protobuf==5.27.2
+protobuf==5.27.3
     # via streamlit
-pyarrow==16.1.0
+pyarrow==17.0.0
     # via streamlit
 pydeck==0.9.1
     # via streamlit
@@ -103,14 +104,14 @@ requests==2.32.3
     # via streamlit
 rich==13.7.1
     # via streamlit
-rpds-py==0.19.0
+rpds-py==0.19.1
     # via jsonschema
     # via referencing
 six==1.16.0
     # via python-dateutil
 smmap==5.0.1
     # via gitdb
-streamlit==1.36.0
+streamlit==1.37.0
     # via pygenomeviz
 tenacity==8.5.0
     # via streamlit

src/pygenomeviz/__init__.py

@@ -2,7 +2,7 @@
 
 from pygenomeviz.genomeviz import GenomeViz
 
-__version__ = "1.2.1"
+__version__ = "1.3.0"
 
 __all__ = [
     "GenomeViz",

src/pygenomeviz/align/tool/base.py

@@ -11,7 +11,7 @@
 
 from pygenomeviz.align import AlignCoord
 from pygenomeviz.logger import get_logger
-from pygenomeviz.parser import Genbank
+from pygenomeviz.parser import Fasta, Genbank
 
 
 class AlignToolBase(ABC):
@@ -156,25 +156,25 @@ def _parse_input_gbk_seqs(
         return parse_seqs
 
     def _parse_input_gbk_and_fasta_seqs(
-        self, seqs: Sequence[str | Path | Genbank]
-    ) -> Sequence[Path | Genbank]:
+        self, seqs: Sequence[str | Path | Fasta | Genbank]
+    ) -> Sequence[Fasta | Genbank]:
         """Parse input genbank and fasta sequences
 
         Parameters
         ----------
-        seqs : Sequence[str | Path | Genbank]
-            List of `fasta file` or `genbank file` or `Genbank object`
+        seqs : Sequence[str | Path | Fasta | Genbank]
+            List of fasta or genbank
 
         Returns
         -------
-        parse_seqs : Sequence[Path | Genbank]
-            List of `fasta file` or `Genbank object`
+        parse_seqs : Sequence[Fasta | Genbank]
+            List of fasta or genbank
         """
         # Check number of seqs
         if len(seqs) < 2:
             raise ValueError("Number of input seqs is less than 2.")
         # Parse genbank or fasta files
-        parse_seqs: Sequence[Path | Genbank] = []
+        parse_seqs: Sequence[Fasta | Genbank] = []
         for seq in seqs:
             if isinstance(seq, str):
                 seq = Path(seq)
@@ -184,7 +184,7 @@ def _parse_input_gbk_and_fasta_seqs(
                 if seq.suffix in gbk_suffixes:
                     parse_seqs.append(Genbank(seq))
                 elif seq.suffix in fasta_suffixes:
-                    parse_seqs.append(seq)
+                    parse_seqs.append(Fasta(seq))
                 else:
                     valid_suffixes = gbk_suffixes + fasta_suffixes
                     err_msg = f"'{seq}' is invalid file suffix ({valid_suffixes=})"

src/pygenomeviz/align/tool/blast.py

@@ -2,14 +2,13 @@
 
 import logging
 import os
-import shutil
 from pathlib import Path
 from tempfile import TemporaryDirectory
 from typing import Sequence, get_args
 
 from pygenomeviz.align import AlignCoord
 from pygenomeviz.align.tool import AlignToolBase
-from pygenomeviz.parser import Genbank
+from pygenomeviz.parser import Fasta, Genbank
 from pygenomeviz.typing import SeqType
 
 
@@ -18,7 +17,7 @@ class Blast(AlignToolBase):
 
     def __init__(
         self,
-        seqs: Sequence[str | Path | Genbank],
+        seqs: Sequence[str | Path | Fasta | Genbank],
         *,
         outdir: str | Path | None = None,
         seqtype: SeqType = "nucleotide",
@@ -31,8 +30,8 @@ def __init__(
         """
         Parameters
         ----------
-        seqs : Sequence[str | Path | Genbank]
-            List of `fasta file` or `genbank file` or `Genbank object`
+        seqs : Sequence[str | Path | Fasta | Genbank]
+            List of fasta or genbank
             (file suffix must be `.fa`, `.fna`, `.fasta`, `.gb`, `.gbk`, `.gbff`)
         outdir : str | Path | None, optional
             Temporary result directory. If None, tmp directory is auto created.
@@ -107,7 +106,7 @@ def run(self) -> list[AlignCoord]:
         return align_coords
 
     def _write_genome_files(self, outdir: str | Path) -> list[Path]:
-        """Write (or copy) genome fasta files to output directory
+        """Write genome fasta files to output directory
 
         Parameters
         ----------
@@ -121,15 +120,10 @@ def _write_genome_files(self, outdir: str | Path) -> list[Path]:
         """
         genome_files: list[Path] = []
         for seq in self._seqs:
-            if isinstance(seq, Genbank):
-                genome_file = Path(outdir) / f"{seq.name}.fna"
-                log_msg = f"Convert Genbank object to genome fasta file '{genome_file}'"
-                self._logger.info(log_msg)
-                seq.write_genome_fasta(genome_file)
-                genome_files.append(genome_file)
-            else:
-                genome_file = Path(outdir) / seq.name
-                self._logger.info(f"Copy genome fasta file to '{genome_file}'")
-                shutil.copy(seq, genome_file)
-                genome_files.append(genome_file)
+            genome_file = Path(outdir) / f"{seq.name}.fna"
+            cls_name = seq.__class__.__name__
+            log_msg = f"Convert {cls_name} object to genome fasta file '{genome_file}'"
+            self._logger.info(log_msg)
+            seq.write_genome_fasta(genome_file)
+            genome_files.append(genome_file)
         return genome_files